The nationwide Magic High Schools Thesis Competition held by the Japan Magic Association. Also known as just The Thesis Competition will be held in Kyoto. After experiencing the Thesis Competition being attacked by the Great Asian Alliance last year, Mikihiko, the head of the Disciplinary Committee, proposes to the Student Council that this year they would like to inspect the area around the venue in advance to ensure security. Tatsuya, Miyuki, Minami, Leo and Erika will also be accompanying him. On his way home after the Student Council meeting, Tatsuya learns from the news that Mayumi's bodyguard, Saburo Nakura, was murdered by someone in Kyoto.

As Tatsuya is researching the Traditionalist bases in Kyoto under Minoru's guidance, he meets the owner of a restaurant, who is also a Traditionalist, on the way to Kiyomizu Temple. The shop owner shares that he is concerned about the current state of Nara's Traditionalist sects being absorbed by casters from the Continent and offers to share information with Tatsuya. Based on the restaurant owner's information, Tatsuya narrows down a place in Kyoto where the Traditionalists are hiding. He meets with Mayumi, who wants to find the culprit who killed Nakura, and Masaki, who happened to come across them during a battle against the Traditionalists, and heads to Arashiyama with them.

The night before the Thesis Competition. Tatsuya receives a report from Fumiya that they have located Gongjin Zhou's whereabouts. He was hiding at the JGDF's 2nd Supply Base in Uji. Tatsuya speculates that he would not have enough offensive power to fight alone at the JGDF's base, so he contacts Masaki. When Masaki hears that they would need to invade an army base to get to him, he hesitates for a moment but decides to accompany Tatsuya to fulfill his responsibilities as a member of the Ten Master Clans. The two invade the army base where soldiers controlled by Gongji Zhou await...

Information gets out that Kanda, an anti-magic advocate and Diet member, will visit First High School with the media to observe the school's curriculum, claiming that he has heard disturbing rumors about it. He plans to create an uproar with the media and assert that the school is brainwashing students into the military - if he finds anything suspicious of that nature. To stop this ploy, Tatsuya suggests performing an experiment showing the students creating a Sustained Gravity Control-Type Magic Thermonuclear Fusion Reactor = Stellar Furnace. The students plan on demonstrating that the magic education they receive at the school can solve energy problems, and that magic can contribute to the peace of humankind depending on the type of magic they use.

Tatsuya and Miyuki are invited to a party to commemorate the completion of Japan's first hyper-building offshore tower, there Hayama introduces a young girl called Sakurai Minami. The two are shaken upon seeing her face which is that of a woman who died in an incident three years earlier. At such a time, there is intelligence that the party is being targeted by extremist magic advocates — The Advancement of Humanity Front.

A brother and a sister enroll at the Magic High School. In this school, the students are divided into two distinct groups as "Weeds" and "Blooms." Tatsuya, the brother, has a secret…

The Advancement of Humanity Front have declared they will ‘blow up the offshore tower in one hour’. But there is no guarantee they will keep to their one-hour time limit. For the sake of preventing the Advancement of Humanity Front’s scheme, Tatsuya takes Miyuki and Minami towards the control centre on the first underground floor.

News outlets were enthusiastically reporting the great success of the stellar furnace experiment carried out by the students at First High School. However, since Takuma Shippou had heard from his father that the Saegusa Family was going to be the ones to deal with Diet member Kanda, he thinks they used Tatsuya to claim credit for the experiment's success themselves. Takuma then takes his pent-up anger out on Kasumi Saegusa, who he happened to pass by on campus. Kasumi, unable to turn a blind eye to these insults against her family, is on the brink of engaging in a magic fight with Takuma... But then, the Disciplinary Committee intervenes before either of them makes their move, and takes them in for questioning. Tatsuya suggests they let them duke it out in an official match to end this mutual enmity between the two once and for all.

A notice has been sent to the magic high schools across the country that a portion of the events in the Nine Schools Competition will be changed. Shockingly, three of the six events will be changed. In order to respond to the sudden change in events, First High School's Student Council is thrown in a frenzy to understand the new rules, reselecting athletes and readjusting their CADs. While everyone was complaining about the Competition's management due to the sudden change in timing, one month before the start of the Nine Schools Competition, Tatsuya had a growing suspicion about the strong military flavor of all the newly added events.

Tatsuya and the other Student Council members were spending their days extremely busy in order to deal with the sudden change of events for the Nine Schools Competition. However, out of the blue, Tatsuya receives an email from an unknown sender. The email states that the changes in the competition were due to pressure from the JDF, and that the Kudou Family was planning to piggyback on the JDF's order to test out a secretly developed military weapon at the Steeplechase Cross-country Event. This prompts Tatsuya to head to Nara, where the Kudou Family's stronghold is based, to find out more about the experiments they are conducting.

It turns out that the secret experiments that the Kudou Family has been conducting was for developing parasite dolls, a female combat robot possessed by a parasite. Experiments on the dolls' operations are being conducted at the Steeplechase Cross-country venue, where security is abnormally tight - so much so that Tatsuya himself can't even break into the premises. As such, Tatsuya orders Pixie to keep an eye out for the parasites while he conducts adjustments to the CADs and gives instructions to the underclassmen as an engineer. However, this continual sense of nervousness and nonstop days of hard work are tiring out Tatsuya. He's never felt this tired before.

The women's division of the Steeplechase Cross-country Event has finally begun. Tatsuya has Pixie figure out the location of all the parasite dolls and tries to eliminate them before they come into contact with the players. However, the parasite dolls unleash their magic at speeds that exceed Tatsuya's imagination. Though it is difficult, he manages to seal away the first parasite doll. Tatsuya goes on to seal away the remaining parasite dolls one after another, but the highest-performance models, the Prime Four, now stand in his way.

In order to obtain cooperation from Retsu Kudou to capture Gongjin Zhou, Tatsuya, Miyuki and Minami visit Nara, the home of the Kudou Family. Retsu Kudou readily accepts Tatsuya's offer and introduces him to his grandson, Minoru. Minoru is one year Tatsuya's junior, and although he is physically weak, he is said to be a very powerful magician. At the dinner table, Minoru hears that Tatsuya and his friends are looking for a traditional magic user and offers his help. The next day, as Tatsuya and the others are scouting the Traditionalists' base in Nara under Minoru's guidance, they are attacked by the Traditionalists at Nara Park.

Mibu meets with Tatsuya at a cafe. She thanks him for defusing the brawl between her and Kirihara peacefully. She asks Tatsuya to join their kendo team. He suspects that she has an ulterior motive…

Thanks to Pixie's psychic powers, Tatsuya and his friends are finally able to capture the parasites. They leave the scene after Erika and her team arrive, but a third faction disguised as the police appear before them and get in their way.

About a month after the parasite incident, Tatsuya and his friends reluctantly bid farewell to Mayumi, Mari, Katsuto and the other seniors at the 29th graduation ceremony at First High School. The time also comes for them to give a send-off to another friend who came from America.

A string of bizarre murders occurred where the victims were found to have most of the blood drawn from their bodies. Due to the methods used by the killer, they were called "vampire incidents," and similar incidents were also occurring in America.

Nine Schools Competition has finally started, and all eyes are on First High School. Tatsuya learns that the intruders from previous night are with the No-Head Dragons. Will the competition continue without any more interruption?

During Women's Battle Board, Mari Watanabe has an accident and is taken to the Susono Base Hospital. Tatsuya helps her recover with magic. Still, she has to withdraw from Mirage Bat. Tatsuya suspects that the accident wasn't just an accident at all!

During the preparations for the Thesis Competition, a girl is seen carrying a wireless password breaker. Erika offers to teach Leo a move that would be lethal against his enemies. Since they are taking the day off together, rumors start flying about them!

The President of the Student Council invites Miyuki and Tatsuya to lunch. During lunch, she asks Miyuki to join the Student Council. Miyuki says that her brother should also join them. Will he have to prove himself?

Lately, Tatsuya has been reading about creating the Philosopher's Stone, thinking that it might have the capability to store Magic Sequences. Surprisingly, he is asked to participate in the Thesis Competition as a member of the First High School team.

The vampire that attacked Leo was a demon called a "parasite." The Saegusa and Jumonji families decide to join forces to solve this case. Mikihiko and Erika search for the parasite to get revenge for Leo, and they confront a mysterious masked magician.

It has reached the month of April in 2096, and various aspects of Tatsuya's life was changing as he advances to the second year. Tatsuya and Mizuki transferred to the newly established Department of Magical Engineering, and Mikihiko has also transferred out of Course 2, and was now a Course 1 student. Along with this change, Tatsuya and Miyuki were now living with Minami who was sent to stay with them by the Yotsuba Family. Tatsuya enters the school year hoping they would have a peaceful student life this time around, but the new year meant the arrival of new students, like Kasumi and Izumi, the twins of the Sagusa Family, and Takuma Shippou, the new student valedictorian who feels a rivalry towards the Saegusa Family. All of them having their own quirk or two, for better or for worse...

The entrance ceremony has ended, and club recruitment of the freshmen has begun. Amidst the competitive recruitment frenzy, the Robot Research Club and Motorcycle Club were getting in a heated stare off over a freshman that both clubs were aiming to recruit. Kasumi, from the Disciplinary Committee, and Shippou, from the Extracurricular Activities Federation, intervene. However, now the two who had come to break up the fight begin arguing amongst themselves over who should have authority over the situation, and were on the brink of initiating a physical fight. Meanwhile, Koichi, the head of the Saegusa Family, was devising a plan to mitigate the Yotsuba Family's power through a false anti-magician campaign that the USNA's Humanist Extremist group was drawing up for the media.